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statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
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error when there is NA for allele frequency #182

Closed jielab closed 2 years ago

jielab commented 2 years ago

Hi, there:

I got a pheweb error when my GWAS's "af" column has NA values, sometimes all NA values.

Is there a way to accommodate NA values for "af"?

Thank you & best regards, Jie

pjvandehaar commented 2 years ago

Please send screenshot of error, file, and pheweb -v

On Sun, Oct 24, 2021 at 2:35 AM Jie Huang @.***> wrote:

Hi, there:

I got a pheweb error when my GWAS's "af" column has NA values, sometimes all NA values.

Is there a way to accommodate NA values for "af"?

Thank you & best regards, Jie

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jielab commented 2 years ago

Dear Peter:

The error message is simply a short line of text. You will easily replicate this error, when your input GWAS has a column named "AF" with all NA values, and then your config.py file has 'AF': 'af'. Then Pheweb will complain that AF is not numerical.

The add_rsID function is really cool. Previously I commented that you guys could simply add a brief line to the end of your add_rsid.py script so that it does not force REF/ALT in your GWAS must be the same as that in the so-called reference genome. Most GWAS these days don't have REF/ALT, but only EA/NEA or A1/A2. It would be good that you guys could make add_rsid.py to accommodate this. Right now, most rsID are still missing even after add_rsid.

Finally, since pheweb could add_rsID, is it possible to add_Chr&POS if the input GWAS only has rsID?

Best regards, Jie